Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Vitis vinifera

ABSTRACT: Genome-wide expression profiling of grapevine (Vitis vinifera cv Cabernet Sauvignon) woody stems and asymptomatic leaves during a time course of infection by Neofusicoccum parvum

PROVIDER: PRJNA383160 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR5453840.fastq.gz	Fastqsanger.gz
	SRR5453850.fastq.gz	Fastqsanger.gz
	SRR5453860.fastq.gz	Fastqsanger.gz
	SRR5453870.fastq.gz	Fastqsanger.gz
	SRR5453880.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 126

Similar Datasets

E-GEOD-97900

Project description:Genome-wide expression profiling of grapevine (Vitis vinifera cv Cabernet Sauvignon) woody stems and asymptomatic leaves during a time course of infection by Neofusicoccum parvum

2020-04-17 | E-GEOD-97900 | ExpressionAtlas

V. vinifera 'Cabernet sauvignon' and V. aestivalis 'Norton' innoculated with Erysiphe necator conidiospores

Project description:we analyzed pathogen-induced changes in the transcriptome of Vitis vinifera ‘Cabernet sauvignon’ and Vitis aestivalis ‘Norton’ by conducting a large-scale study to measure transcript abundance at 0, 4, 8, 12, 24, and 48 hours post-treatment in conidiospore- and mock-inoculated leaves using Affymetrix GeneChip Vitis vinifera Genome Array Keywords: time course

2007-11-29 | GSE6404 | GEO

Auto-grafting in grapevine 3 and 28 days after grafting

Project description:The analysis of the genes differentially expressed in the rootstock and the callus 3 and 28 d after grafting in grapevine (Vitis vinifera cv Cabernet Sauvignon) auto-grafts.

2013-05-31 | E-MEXP-3803 | biostudies-arrayexpress

Host-based markers for the early stage of infection by the grapevine trunk pathogen Neofusicoccum parvum

Project description:In the vineyard, symptoms of the grapevine trunk disease Botryosphaeria dieback do not appear until 1 or 2 years after the causal fungus Neofusicoccum parvum establishes a necrotic canker in the permanent woody structure of the vine. There are preventative management practices, but growers tend to wait until symptoms are widespread, at which point prevention has limited efficacy. Toward development of an early detection tool, we examined the leaves of inoculated vs. non-inoculated plants for differential gene expression via RNASeq. Stems were examined to monitor spread of the infection, and its spatial and temporal relationship to anatomical changes via light microscopy and high resolution computed tomography (HRCT). The early stage of infection occurred prior to 2 months post-inoculation (MPI), at which point spread of the pathogen beyond the inoculation site was greatest. This incubation period was also characterized by the largest stem lesions, the highest levels of fungal colonization and xylem vessels fully-occluded by gels, and the lowest starch content of xylem fibers and rays. Prior to 2 MPI, RNASeq and validative qPCR analysis identified eight candidate markers, which are transcriptionally activated by infection, but not by wounding alone. Our best marker genes, a dehydrin, a BURP domain containing protein and an abscissic acid-induced wheat plasma membrane polypeptide 19 (AWPM-19), identified the pathogenâ??s presence with high specificity. Screening of genome-wide expression data revealed that this signature is not affected by many abiotic and biotic stresses. Asymptomatic leaf mRNA profiles of Neofusicoccum parvum infected wounded plants (IW) and non-infected wounded plants (NIW) at two different time points post inoculation (0 MPI, 0.5-1.5 MPI) were generated by deep sequencing in biological triplicates using Illumina HiSeq2500 technology.

2015-03-24 | E-GEOD-58653 | biostudies-arrayexpress

Vitis vinifera

Project description:Grapevine (Vitis vinifera, cabernet sauvignon) small RNA sequencing reads from bud tissue

| PRJNA955780 | ENA

genome sequence of the grapevine cultivar Vitis vinifera ‘Cabernet Sauvignon’

Project description:genome sequence of the grapevine cultivar Vitis vinifera ‘Cabernet Sauvignon’

| PRJEB94081 | ENA

Gene expression during graft union formation in auto- and hetero-grafts of grapevine

Project description:Transcriptional changes occurring at the graft interface of auto- (Cabernet Sauvignon/ Cabernet Sauvignon) and hetero-grafted (Cabernet Sauvignon/ Riparia Gloire de Montpellier and Cabernet Sauvignon /1103 Paulsen) grapevine. Gene expression profiling was done using the Nimblegen whole genome array with 3 biological replicates of 15 pooled graft interfaces harvested 3, 7, 14 and 28 d after grafting.

2014-04-09 | E-MTAB-1610 | biostudies-arrayexpress

Transcription profiling of Vitis vinifera cv. Cabernet-Sauvignon leaves obtained from plants grown in different enviroments and infected with vascular ascomycete fungus Eutypa lata.

Project description:Eutypa dieback is a vascular disease that may severely affect vineyards throughout the world. In the present work, microarrays analysis were made in order (i) to improve our knowledge of grapevine (Vitis vinifera cv. Cabernet-Sauvignon) responses to Eutypa lata, the causal agent of Eutypa dieback and (ii) to identify genes that may prevent symptom development. Qiagen/Operon grapevine microarrays bearing 14,500 probes were used to compare between three experimental conditions (in vitro, greenhouse, vineyard), foliar material of infected symptomatic plants (S+R+), infected asymptomatic plants (S-R+), and healthy plants (S-R-). These plants were characterized by symptoms notation after natural (vineyard) or experimental (in vitro, greenhouse) infection, re-isolation of the fungus located in the lignified parts, and the formal identification of E. lata mycelium by PCR. Semi-quantitative RT-PCR experiments were run to confirm the expression of some genes of interest in response to E. lata. Their expression profiles were also studied in response to other grapevine pathogens (E. necator, P. viticola, B. cinerea). (i) Five functional categories including metabolism, defense reactions, interaction with environment, transport and transcription were up-regulated in S+R+ plants compared to S-R- plants. These genes, which cannot prevent infection and symptom development, are not specific since they were also upregulated after infection by powdery mildew, downy mildew and black rot. (ii) Most of the genes that may prevent symptom development are associated with the light phase of photosynthesis. This finding is discussed in the context of previous data on the mode of action of eutypin and Eutypa secreted polypeptide fraction.

2010-03-01 | E-MEXP-2337 | biostudies-arrayexpress

Diel multi-tissue genome-scale metabolic models of Vitis vinifera

Project description:The first GSSM of V. vinifera was reconstructed (MODEL2408120001). Tissue-specific models for stem, leaf, and berry of the Cabernet Sauvignon cultivar were generated from the original model, through the integration of RNA-Seq data. These models have been merged into diel multi-tissue models to study the interactions between tissues at light and dark phases.

2024-09-02 | MODEL2408160001 | BioModels

Grape skin transcriptome to reveal genes related with resveratrol accumulation

Project description:Methods:transcriptomes of the different development stages of Vitis vinifera cv. Cabernet Sauvignon and Vitis quinquangularis accession Danfeng-2 were analyzed using Illumina Hiseq 2500. The sequence reads that passed quality filters were analyzed: TopHat followed by Cufflinks. mRNA profiles of different development stages of Vitis vinifera cv. Cabernet Sauvignon and Vitis quinquangularis accession Danfeng-2 were generated by deep sequencing, in triplicate, using Illumina Hiseq 2500.

2015-12-23 | E-GEOD-76256 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data